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Scaffold, Villager, BioCyc, Star-P 2.5 for Python, eMolecules, BioPathwise DM

Geneva Bioinformatics and Proteome Software have integrated GeneBio’s Phenyx software platform for mass spectrometry data analysis into Proteome’s Scaffold proteomics meta-analysis software. The integration gives users increased access to available results, the companies said.
Phenyx identifies and characterizes proteins and peptides from MS data, while
Scaffold statistically validates peptides and proteins from tandem mass spectrometry results. Scaffold considers the results form multiple search engines including Phenyx, Sequest, or Mascot, as well as optionally running X!Tandem on data files for cross-validation.

Transgenic Software has announced a Microsoft SQL Server 2005 version of its Villager Transgenic Animal Management System, a laboratory information-management system that develops, breeds, and tracks transgenic and knockout animal models.
The server version furthers the company’s transgenic workflow control technology and bolsters integration with the Microsoft Office development platform, the company said.

SRI International has released version 11.1 of the BioCyc suite of databases. EcoCyc 11.1 includes six new metabolic pathways, while MetaCyc 11.1 has been enhanced to offer 39 new pathways and 31 revised pathways that include new commentary and updated enzyme and gene identification. MetaCyc also includes a new “superpathway,” for a combined 71 new and updated pathways. 
The new version also expands coverage of fermentation pathways; the metabolism of glutamate, glutamine, aspartate, and asparagine; and the degradation of parathion and related compounds.

Interactive Supercomputing has launched Star-P 2.5 for Python, a new version of its parallel computing software that is compatible with the open source programming language Python.
Star-P for Python enables users to code algorithms on their desktops using Python, but run them on parallel high performance computers, ISC said. It includes a new client interface that lets users take advantage of Python-specific numerical libraries and functions such as NumPy and SciPy.
Python is the second major programming client supported by Star-P, following the platform’s current support for Matlab.
Star-P 2.5 for Python will ship at the end of June and starts at $7,995 for commercial users and $2,495 for academic institutions.
More information is available here.

eMolecules has released version 2.0 of its freely available chemical search engine. Available here, version 2 includes an improved user interface and more than 6 million compounds from 150 suppliers, the company said.   

The BioAnalytics Group has launched BioPathwise DM, a data-management software package for biological data.The server-based system enables groups of researchers to store, and share data along with any reports, records, peer-reviewed journals, or other information.

Filed under

The Scan

Missed Early Cases

A retrospective analysis of blood samples suggests early SARS-CoV-2 infections may have been missed in the US, the New York Times reports.

Limited Journal Editor Diversity

A survey finds low diversity among scientific and medical journal editors, according to The Scientist.

How Much of a Threat?

Science writes that need for a provision aimed at shoring up genomic data security within a new US bill is being questioned.

PNAS Papers on Historic Helicobacter Spread, Brain Development, C. difficile RNAs

In PNAS this week: Helicobacter genetic diversity gives insight into human migrations, gene expression patterns of brain development, and more.